nabu 2024.1.0rc4__py3-none-any.whl → 2024.1.1__py3-none-any.whl

build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/tests/test_z_stitching.py

@@ -0,0 +1,1183 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+__authors__ = ["H. Payno"]
+__license__ = "MIT"
+__date__ = "13/05/2022"
+
+
+import os
+from silx.image.phantomgenerator import PhantomGenerator
+from scipy.ndimage import shift as scipy_shift
+import numpy
+import pytest
+from nabu.stitching.config import (
+    PreProcessedZStitchingConfiguration,
+    PostProcessedZStitchingConfiguration,
+)
+from nabu.utils import Progress
+from nabu.stitching.config import KEY_IMG_REG_METHOD, NormalizationBySample
+from nabu.stitching.overlap import ZStichOverlapKernel, OverlapStitchingStrategy
+from nabu.stitching.z_stitching import (
+    PostProcessZStitcher,
+    PreProcessZStitcher,
+    stitch_vertically_raw_frames,
+    ZStitcher,
+)
+from nxtomo.nxobject.nxdetector import ImageKey
+from nxtomo.utils.transformation import UDDetTransformation, LRDetTransformation
+from nxtomo.application.nxtomo import NXtomo
+from nabu.stitching.alignment import AlignmentAxis1, AlignmentAxis2
+from tomoscan.factory import Factory as TomoscanFactory
+from tomoscan.utils.volume import concatenate as concatenate_volumes
+from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
+from tomoscan.esrf.volume import HDF5Volume, EDFVolume
+from tomoscan.esrf.volume.jp2kvolume import JP2KVolume, has_minimal_openjpeg
+from tomoscan.esrf.volume.tiffvolume import TIFFVolume, has_tifffile
+from nabu.stitching.utils import ShiftAlgorithm
+import h5py
+
+
+strategies_to_test_weights = (
+    OverlapStitchingStrategy.CLOSEST,
+    OverlapStitchingStrategy.COSINUS_WEIGHTS,
+    OverlapStitchingStrategy.LINEAR_WEIGHTS,
+    OverlapStitchingStrategy.MEAN,
+)
+
+
+def build_raw_volume():
+    """util to create some raw volume"""
+    raw_volume = numpy.stack(
+        [
+            PhantomGenerator.get2DPhantomSheppLogan(n=120).astype(numpy.float32) * 256.0,
+            PhantomGenerator.get2DPhantomSheppLogan(n=120).astype(numpy.float32) * 128.0,
+            PhantomGenerator.get2DPhantomSheppLogan(n=120).astype(numpy.float32) * 32.0,
+            PhantomGenerator.get2DPhantomSheppLogan(n=120).astype(numpy.float32) * 16.0,
+        ]
+    )
+    assert raw_volume.shape == (4, 120, 120)
+    raw_volume = numpy.rollaxis(raw_volume, axis=1, start=0)
+    assert raw_volume.shape == (120, 4, 120)
+    return raw_volume
+
+
+@pytest.mark.parametrize("strategy", strategies_to_test_weights)
+def test_overlap_z_stitcher(strategy):
+    frame_width = 128
+    frame_height = frame_width
+    frame_1 = PhantomGenerator.get2DPhantomSheppLogan(n=frame_width)
+    stitcher = ZStichOverlapKernel(
+        stitching_strategy=strategy,
+        overlap_size=frame_height,
+        frame_width=128,
+    )
+    stitched_frame = stitcher.stitch(frame_1, frame_1)[0]
+    assert stitched_frame.shape == (frame_height, frame_width)
+    # check result is close to the expected one
+    numpy.testing.assert_allclose(frame_1, stitched_frame, atol=10e-10)
+
+    # check sum of weights ~ 1.0
+    numpy.testing.assert_allclose(
+        stitcher.weights_img_1 + stitcher.weights_img_2,
+        numpy.ones_like(stitcher.weights_img_1),
+    )
+
+
+@pytest.mark.parametrize("dtype", (numpy.float16, numpy.float32))
+def test_z_stitch_raw_frames(dtype):
+    """
+    test z_stitch_raw_frames: insure a stitching with 3 frames and different overlap can be done
+    """
+    ref_frame_width = 256
+    frame_ref = PhantomGenerator.get2DPhantomSheppLogan(n=ref_frame_width).astype(dtype)
+
+    # split the frame into several part
+    frame_1 = frame_ref[0:100]
+    frame_2 = frame_ref[80:164]
+    frame_3 = frame_ref[154:]
+
+    kernel_1 = ZStichOverlapKernel(frame_width=ref_frame_width, overlap_size=20)
+    kernel_2 = ZStichOverlapKernel(frame_width=ref_frame_width, overlap_size=10)
+
+    stitched = stitch_vertically_raw_frames(
+        frames=(frame_1, frame_2, frame_3),
+        output_dtype=dtype,
+        overlap_kernels=(kernel_1, kernel_2),
+        raw_frames_compositions=None,
+        overlap_frames_compositions=None,
+        key_lines=(
+            (
+                90,  # frame_1 height - kernel_1 height / 2.0
+                10,  # kernel_1 height / 2.0
+            ),
+            (
+                79,  # frame_2 height - kernel_2 height / 2.0 ou 102-20 ?
+                5,  # kernel_2 height / 2.0
+            ),
+        ),
+    )
+
+    assert stitched.shape == frame_ref.shape
+    numpy.testing.assert_array_almost_equal(frame_ref, stitched)
+
+
+def test_z_stitch_raw_frames_2():
+    """
+    test z_stitch_raw_frames: insure a stitching with 3 frames and different overlap can be done
+    """
+    ref_frame_width = 256
+    frame_ref = PhantomGenerator.get2DPhantomSheppLogan(n=ref_frame_width).astype(numpy.float32)
+
+    # split the frame into several part
+    frame_1 = frame_ref.copy()
+    frame_2 = frame_ref.copy()
+    frame_3 = frame_ref.copy()
+
+    kernel_1 = ZStichOverlapKernel(frame_width=ref_frame_width, overlap_size=10)
+    kernel_2 = ZStichOverlapKernel(frame_width=ref_frame_width, overlap_size=10)
+
+    stitched = stitch_vertically_raw_frames(
+        frames=(frame_1, frame_2, frame_3),
+        output_dtype=numpy.float32,
+        overlap_kernels=(kernel_1, kernel_2),
+        raw_frames_compositions=None,
+        overlap_frames_compositions=None,
+        key_lines=((20, 20), (105, 105)),
+    )
+
+    assert stitched.shape == frame_ref.shape
+    numpy.testing.assert_array_almost_equal(frame_ref, stitched)
+
+
+_stitching_configurations = (
+    # simple case where shifts are provided
+    {
+        "n_proj": 4,
+        "raw_pos": ((0, 0, 0), (-90, 0, 0), (-180, 0, 0)),  # requested shift to
+        "input_pos": ((0, 0, 0), (-90, 0, 0), (-180, 0, 0)),  # requested shift to
+        "raw_shifts": ((0, 0), (-90, 0), (-180, 0)),
+    },
+    # simple case where shift is found from z position
+    {
+        "n_proj": 4,
+        "raw_pos": ((90, 0, 0), (0, 0, 0), (-90, 0, 0)),
+        "input_pos": ((90, 0, 0), (0, 0, 0), (-90, 0, 0)),
+        "check_bb": ((40, 140), (-50, 50), (-140, -40)),
+        "axis_0_params": {
+            KEY_IMG_REG_METHOD: ShiftAlgorithm.NONE,
+        },
+        "axis_2_params": {
+            KEY_IMG_REG_METHOD: ShiftAlgorithm.NONE,
+        },
+        "raw_shifts": ((0, 0), (-90, 0), (-180, 0)),
+    },
+)
+
+
+@pytest.mark.parametrize("configuration", _stitching_configurations)
+@pytest.mark.parametrize("dtype", (numpy.float32, numpy.int16))
+def test_PreProcessZStitcher(tmp_path, dtype, configuration):
+    """
+    test PreProcessZStitcher class and insure a full stitching can be done automatically.
+    """
+    n_proj = configuration["n_proj"]
+    ref_frame_width = 280
+    raw_frame_height = 100
+    ref_frame = PhantomGenerator.get2DPhantomSheppLogan(n=ref_frame_width).astype(dtype) * 256.0
+
+    # add some mark for image registration
+    ref_frame[:, 96] = -3.2
+    ref_frame[:, 125] = 9.1
+    ref_frame[:, 165] = 4.4
+    ref_frame[:, 200] = -2.5
+    # create raw data
+    frame_0_shift, frame_1_shift, frame_2_shift = configuration["raw_shifts"]
+    frame_0 = scipy_shift(ref_frame, shift=frame_0_shift)[:raw_frame_height]
+    frame_1 = scipy_shift(ref_frame, shift=frame_1_shift)[:raw_frame_height]
+    frame_2 = scipy_shift(ref_frame, shift=frame_2_shift)[:raw_frame_height]
+
+    frames = frame_0, frame_1, frame_2
+    frame_0_input_pos, frame_1_input_pos, frame_2_input_pos = configuration["input_pos"]
+    frame_0_raw_pos, frame_1_raw_pos, frame_2_raw_pos = configuration["raw_pos"]
+
+    # create a Nxtomo for each of those raw data
+    raw_data_dir = tmp_path / "raw_data"
+    raw_data_dir.mkdir()
+    output_dir = tmp_path / "output_dir"
+    output_dir.mkdir()
+    z_position = (
+        frame_0_raw_pos[0],
+        frame_1_raw_pos[0],
+        frame_2_raw_pos[0],
+    )
+    scans = []
+    for (i_frame, frame), z_pos in zip(enumerate(frames), z_position):
+        nx_tomo = NXtomo()
+        nx_tomo.sample.z_translation = [z_pos] * n_proj
+        nx_tomo.sample.rotation_angle = numpy.linspace(0, 180, num=n_proj, endpoint=False)
+        nx_tomo.instrument.detector.image_key_control = [ImageKey.PROJECTION] * n_proj
+        nx_tomo.instrument.detector.x_pixel_size = 1.0
+        nx_tomo.instrument.detector.y_pixel_size = 1.0
+        nx_tomo.instrument.detector.distance = 2.3
+        nx_tomo.energy = 19.2
+        nx_tomo.instrument.detector.data = numpy.asarray([frame] * n_proj)
+
+        file_path = os.path.join(raw_data_dir, f"nxtomo_{i_frame}.nx")
+        entry = f"entry000{i_frame}"
+        nx_tomo.save(file_path=file_path, data_path=entry)
+        scans.append(NXtomoScan(scan=file_path, entry=entry))
+
+    # if requested: check bounding box
+    check_bb = configuration.get("check_bb", None)
+    if check_bb is not None:
+        for scan, expected_bb in zip(scans, check_bb):
+            assert scan.get_bounding_box(axis="z") == expected_bb
+    output_file_path = os.path.join(output_dir, "stitched.nx")
+    output_data_path = "stitched"
+    z_stich_config = PreProcessedZStitchingConfiguration(
+        stitching_strategy=OverlapStitchingStrategy.LINEAR_WEIGHTS,
+        overwrite_results=True,
+        axis_0_pos_px=(
+            frame_0_input_pos[0],
+            frame_1_input_pos[0],
+            frame_2_input_pos[0],
+        ),
+        axis_1_pos_px=(
+            frame_0_input_pos[1],
+            frame_1_input_pos[1],
+            frame_2_input_pos[1],
+        ),
+        axis_2_pos_px=(
+            frame_0_input_pos[2],
+            frame_1_input_pos[2],
+            frame_2_input_pos[2],
+        ),
+        axis_0_pos_mm=None,
+        axis_1_pos_mm=None,
+        axis_2_pos_mm=None,
+        input_scans=scans,
+        output_file_path=output_file_path,
+        output_data_path=output_data_path,
+        axis_0_params=configuration.get("axis_0_params", {}),
+        axis_1_params=configuration.get("axis_1_params", {}),
+        axis_2_params=configuration.get("axis_2_params", {}),
+        output_nexus_version=None,
+        slices=None,
+        slurm_config=None,
+        slice_for_cross_correlation="middle",
+        pixel_size=None,
+    )
+    stitcher = PreProcessZStitcher(z_stich_config)
+    output_identifier = stitcher.stitch()
+    assert output_identifier.file_path == output_file_path
+    assert output_identifier.data_path == output_data_path
+
+    created_nx_tomo = NXtomo().load(
+        file_path=output_identifier.file_path,
+        data_path=output_identifier.data_path,
+        detector_data_as="as_numpy_array",
+    )
+
+    assert created_nx_tomo.instrument.detector.data.ndim == 3
+    mean_abs_error = configuration.get("mean_abs_error", None)
+    if mean_abs_error is not None:
+        assert (
+            numpy.mean(numpy.abs(ref_frame - created_nx_tomo.instrument.detector.data[0, :ref_frame_width, :]))
+            < mean_abs_error
+        )
+    else:
+        numpy.testing.assert_array_almost_equal(
+            ref_frame, created_nx_tomo.instrument.detector.data[0, :ref_frame_width, :]
+        )
+
+    # check also other metadata are here
+    assert created_nx_tomo.instrument.detector.distance.value == 2.3
+    assert created_nx_tomo.energy.value == 19.2
+    numpy.testing.assert_array_equal(
+        created_nx_tomo.instrument.detector.image_key_control,
+        numpy.asarray([ImageKey.PROJECTION.PROJECTION] * n_proj),
+    )
+
+    # check configuration has been saved
+    with h5py.File(output_identifier.file_path, mode="r") as h5f:
+        assert "stitching_configuration" in h5f[output_identifier.data_path]
+
+
+slices_to_test_pre = (
+    {
+        "slices": (None,),
+        "complete": True,
+    },
+    {
+        "slices": (("first",), ("middle",), ("last",)),
+        "complete": False,
+    },
+    {
+        "slices": ((0, 1, 2), slice(3, -1, 1)),
+        "complete": True,
+    },
+)
+
+
+@pytest.mark.parametrize("configuration_dist", slices_to_test_pre)
+def test_DistributePreProcessZStitcher(tmp_path, configuration_dist):
+    slices = configuration_dist["slices"]
+    complete = configuration_dist["complete"]
+
+    n_projs = 100
+    raw_data = numpy.arange(100 * 128 * 128).reshape((100, 128, 128))
+
+    # create raw data
+    frame_0 = raw_data[:, 60:]
+    assert frame_0.ndim == 3
+    frame_0_pos = 40
+    frame_1 = raw_data[:, 0:80]
+    assert frame_1.ndim == 3
+    frame_1_pos = 94
+    frames = (frame_0, frame_1)
+    z_positions = (frame_0_pos, frame_1_pos)
+
+    # create a Nxtomo for each of those raw data
+    raw_data_dir = tmp_path / "raw_data"
+    raw_data_dir.mkdir()
+    output_dir = tmp_path / "output_dir"
+    output_dir.mkdir()
+
+    scans = []
+    for (i_frame, frame), z_pos in zip(enumerate(frames), z_positions):
+        nx_tomo = NXtomo()
+        nx_tomo.sample.z_translation = [z_pos] * n_projs
+        nx_tomo.sample.rotation_angle = numpy.linspace(0, 180, num=n_projs, endpoint=False)
+        nx_tomo.instrument.detector.image_key_control = [ImageKey.PROJECTION] * n_projs
+        nx_tomo.instrument.detector.x_pixel_size = 1.0
+        nx_tomo.instrument.detector.y_pixel_size = 1.0
+        nx_tomo.instrument.detector.distance = 2.3
+        nx_tomo.energy = 19.2
+        nx_tomo.instrument.detector.data = frame
+
+        file_path = os.path.join(raw_data_dir, f"nxtomo_{i_frame}.nx")
+        entry = f"entry000{i_frame}"
+        nx_tomo.save(file_path=file_path, data_path=entry)
+        scans.append(NXtomoScan(scan=file_path, entry=entry))
+
+    stitched_nx_tomo = []
+    for s in slices:
+        output_file_path = os.path.join(output_dir, "stitched_section.nx")
+        output_data_path = f"stitched_{s}"
+        z_stich_config = PreProcessedZStitchingConfiguration(
+            axis_0_pos_px=z_positions,
+            axis_1_pos_px=None,
+            axis_2_pos_px=(0, 0),
+            axis_0_pos_mm=None,
+            axis_1_pos_mm=None,
+            axis_2_pos_mm=None,
+            axis_0_params={},
+            axis_1_params={},
+            axis_2_params={},
+            stitching_strategy=OverlapStitchingStrategy.CLOSEST,
+            overwrite_results=True,
+            input_scans=scans,
+            output_file_path=output_file_path,
+            output_data_path=output_data_path,
+            output_nexus_version=None,
+            slices=s,
+            slurm_config=None,
+            slice_for_cross_correlation="middle",
+            pixel_size=None,
+        )
+        stitcher = PreProcessZStitcher(z_stich_config)
+        output_identifier = stitcher.stitch()
+        assert output_identifier.file_path == output_file_path
+        assert output_identifier.data_path == output_data_path
+
+        created_nx_tomo = NXtomo().load(
+            file_path=output_identifier.file_path,
+            data_path=output_identifier.data_path,
+            detector_data_as="as_numpy_array",
+        )
+        stitched_nx_tomo.append(created_nx_tomo)
+    assert len(stitched_nx_tomo) == len(slices)
+    final_nx_tomo = NXtomo.concatenate(stitched_nx_tomo)
+    assert isinstance(final_nx_tomo.instrument.detector.data, numpy.ndarray)
+    final_nx_tomo.save(
+        file_path=os.path.join(output_dir, "final_stitched.nx"),
+        data_path="entry0000",
+    )
+
+    if complete:
+        len(final_nx_tomo.instrument.detector.data) == 128
+        # test middle
+        numpy.testing.assert_array_almost_equal(raw_data[1], final_nx_tomo.instrument.detector.data[1, :, :])
+    else:
+        len(final_nx_tomo.instrument.detector.data) == 3
+        # test middle
+        numpy.testing.assert_array_almost_equal(raw_data[49], final_nx_tomo.instrument.detector.data[1, :, :])
+    # in the case of first, middle and last frames
+    # test first
+    numpy.testing.assert_array_almost_equal(raw_data[0], final_nx_tomo.instrument.detector.data[0, :, :])
+
+    # test last
+    numpy.testing.assert_array_almost_equal(raw_data[-1], final_nx_tomo.instrument.detector.data[-1, :, :])
+
+
+_VOL_CLASSES_TO_TEST_FOR_POSTPROC_STITCHING = [HDF5Volume, EDFVolume]
+# avoid testing glymur because doesn't handle float
+# if has_minimal_openjpeg:
+#     _VOL_CLASSES_TO_TEST_FOR_POSTPROC_STITCHING.append(JP2KVolume)
+if has_tifffile:
+    _VOL_CLASSES_TO_TEST_FOR_POSTPROC_STITCHING.append(TIFFVolume)
+
+
+@pytest.mark.parametrize("progress", (None, Progress("z-stitching")))
+@pytest.mark.parametrize("volume_class", (_VOL_CLASSES_TO_TEST_FOR_POSTPROC_STITCHING))
+def test_PostProcessZStitcher(
+    tmp_path,
+    volume_class,
+    progress,
+):
+    """
+    test PreProcessZStitcher class and insure a full stitching can be done automatically.
+
+    :param bool clear_input_volumes_data: if True save the volume then clear volume.data (used to check internal management of loading volumes - used to check behavior with HDF5)
+    :param volume_class: class to be used (same class for input and output for now)
+    :param axis_0_pos: position of the different TomoObj along axis 0 (Also know as z axis)
+    """
+    # create some random data.
+    raw_volume = build_raw_volume()
+
+    # create folder to save data (and debug)
+    raw_data_dir = tmp_path / "raw_data"
+    raw_data_dir.mkdir()
+    output_dir = tmp_path / "output_dir"
+    output_dir.mkdir()
+
+    # create a simple case where the volume have 10 voxel of overlap and a height (z) of 30 Voxels, 40 and 30 Voxels
+    vol_1_constructor_params = {
+        "data": raw_volume[0:30, :, :],
+        "metadata": {
+            "processing_options": {
+                "reconstruction": {
+                    "position": (-15.0, 0.0, 0.0),
+                    "voxel_size_cm": (100.0, 100.0, 100.0),
+                }
+            },
+        },
+    }
+
+    vol_2_constructor_params = {
+        "data": raw_volume[20:80, :, :],
+        "metadata": {
+            "processing_options": {
+                "reconstruction": {
+                    "position": (-50.0, 0.0, 0.0),
+                    "voxel_size_cm": (100.0, 100.0, 100.0),
+                }
+            },
+        },
+    }
+
+    vol_3_constructor_params = {
+        "data": raw_volume[60:, :, :],
+        "metadata": {
+            "processing_options": {
+                "reconstruction": {
+                    "position": (-90.0, 0.0, 0.0),
+                    "voxel_size_cm": (100.0, 100.0, 100.0),
+                }
+            },
+        },
+    }
+
+    raw_volumes = []
+    axis_0_positions = []
+    for i_vol, vol_params in enumerate([vol_1_constructor_params, vol_2_constructor_params, vol_3_constructor_params]):
+        if volume_class == HDF5Volume:
+            vol_params.update(
+                {
+                    "file_path": os.path.join(raw_data_dir, f"raw_volume_{i_vol}.hdf5"),
+                    "data_path": "volume",
+                }
+            )
+        else:
+            vol_params.update(
+                {
+                    "folder": os.path.join(raw_data_dir, f"raw_volume_{i_vol}"),
+                }
+            )
+        axis_0_positions.append(vol_params["metadata"]["processing_options"]["reconstruction"]["position"][0])
+
+        volume = volume_class(**vol_params)
+        volume.save()
+        raw_volumes.append(volume)
+
+    volume_1, volume_2, volume_3 = raw_volumes
+
+    output_volume = HDF5Volume(
+        file_path=os.path.join(output_dir, "stitched_volume.hdf5"),
+        data_path="stitched_volume",
+    )
+
+    z_stich_config = PostProcessedZStitchingConfiguration(
+        stitching_strategy=OverlapStitchingStrategy.LINEAR_WEIGHTS,
+        overwrite_results=True,
+        input_volumes=(volume_1, volume_2, volume_3),
+        output_volume=output_volume,
+        slices=None,
+        slurm_config=None,
+        axis_0_pos_px=axis_0_positions,
+        axis_0_pos_mm=None,
+        axis_0_params={"img_reg_method": ShiftAlgorithm.NONE},
+        axis_1_pos_px=None,
+        axis_1_pos_mm=None,
+        axis_1_params={"img_reg_method": ShiftAlgorithm.NONE},
+        axis_2_pos_px=None,
+        axis_2_pos_mm=None,
+        axis_2_params={"img_reg_method": ShiftAlgorithm.NONE},
+        slice_for_cross_correlation="middle",
+        voxel_size=None,
+    )
+
+    stitcher = PostProcessZStitcher(z_stich_config, progress=progress)
+    output_identifier = stitcher.stitch()
+    assert output_identifier.file_path == output_volume.file_path
+    assert output_identifier.data_path == output_volume.data_path
+
+    output_volume.data = None
+    output_volume.metadata = None
+    output_volume.load_data(store=True)
+    output_volume.load_metadata(store=True)
+
+    assert raw_volume.shape == output_volume.data.shape
+
+    numpy.testing.assert_array_almost_equal(raw_volume, output_volume.data)
+
+    metadata = output_volume.metadata
+    assert metadata["program"] == "nabu-stitching"
+    assert "configuration" in metadata
+    assert output_volume.position[0] == -60.0
+    assert output_volume.pixel_size == (1.0, 1.0, 1.0)
+
+
+slices_to_test_post = (
+    {
+        "slices": (None,),
+        "complete": True,
+    },
+    {
+        "slices": (("first",), ("middle",), ("last",)),
+        "complete": False,
+    },
+    {
+        "slices": ((0, 1, 2), slice(3, -1, 1)),
+        "complete": True,
+    },
+)
+
+
+@pytest.mark.parametrize("flip_ud", (True, False))
+@pytest.mark.parametrize("configuration_dist", slices_to_test_post)
+def test_DistributePostProcessZStitcher(tmp_path, configuration_dist, flip_ud):
+    # create some random data.
+    slices = configuration_dist["slices"]
+    complete = configuration_dist["complete"]
+
+    raw_volume = numpy.ones((80, 40, 120), dtype=numpy.float16)
+    raw_volume[:, 0, :] = (
+        PhantomGenerator.get2DPhantomSheppLogan(n=120).astype(numpy.float16)[30:110, :] * 80 * 40 * 120
+    )
+    raw_volume[:, 8, :] = (
+        PhantomGenerator.get2DPhantomSheppLogan(n=120).astype(numpy.float16)[30:110, :] * 80 * 40 * 120 + 2
+    )
+    raw_volume[12] = 1.0
+    raw_volume[:, 23] = 1.2
+    # create folder to save data (and debug)
+    raw_data_dir = tmp_path / "raw_data"
+    raw_data_dir.mkdir()
+    output_dir = tmp_path / "output_dir"
+    output_dir.mkdir()
+
+    def flip_input_data(data):
+        if flip_ud:
+            data = numpy.flipud(data)
+        return data
+
+    volume_1 = HDF5Volume(
+        file_path=os.path.join(raw_data_dir, "volume_1.hdf5"),
+        data_path="volume",
+        data=flip_input_data(raw_volume[-60:, :, :]),
+        metadata={
+            "processing_options": {
+                "reconstruction": {
+                    "position": (-30.0, 0.0, 0.0),
+                    "voxel_size_cm": (100.0, 100.0, 100.0),
+                }
+            },
+        },
+    )
+    volume_1.save()
+
+    volume_2 = HDF5Volume(
+        file_path=os.path.join(raw_data_dir, "volume_2.hdf5"),
+        data_path="volume",
+        data=flip_input_data(raw_volume[:60, :, :]),
+        metadata={
+            "processing_options": {
+                "reconstruction": {
+                    "position": (-50.0, 0.0, 0.0),
+                    "voxel_size_cm": (100.0, 100.0, 100.0),
+                }
+            },
+        },
+    )
+    volume_2.save()
+
+    reconstructed_sub_volumes = []
+    for i_slice, s in enumerate(slices):
+        output_volume = HDF5Volume(
+            file_path=os.path.join(output_dir, f"stitched_subvolume_{i_slice}.hdf5"),
+            data_path="stitched_volume",
+        )
+        volumes = (volume_2, volume_1)
+        z_stich_config = PostProcessedZStitchingConfiguration(
+            stitching_strategy=OverlapStitchingStrategy.LINEAR_WEIGHTS,
+            axis_0_pos_px=tuple(
+                volume.metadata["processing_options"]["reconstruction"]["position"][0] for volume in volumes
+            ),
+            axis_0_pos_mm=None,
+            axis_0_params={},
+            axis_1_pos_px=None,
+            axis_1_pos_mm=None,
+            axis_1_params={},
+            axis_2_pos_px=(0, 0),
+            axis_2_pos_mm=None,
+            axis_2_params={},
+            overwrite_results=True,
+            input_volumes=volumes,
+            output_volume=output_volume,
+            slices=s,
+            slurm_config=None,
+            slice_for_cross_correlation="middle",
+            voxel_size=None,
+            flip_ud=flip_ud,
+        )
+
+        stitcher = PostProcessZStitcher(z_stich_config)
+        vol_id = stitcher.stitch()
+        reconstructed_sub_volumes.append(TomoscanFactory.create_tomo_object_from_identifier(identifier=vol_id))
+
+    final_vol = HDF5Volume(
+        file_path=os.path.join(output_dir, "final_volume"),
+        data_path="volume",
+    )
+    if complete:
+        concatenate_volumes(output_volume=final_vol, volumes=tuple(reconstructed_sub_volumes), axis=1)
+        final_vol.load_data(store=True)
+        with h5py.File("debug.hdf5", mode="w") as h5f:
+            h5f["raw_volume"] = raw_volume
+            h5f["final_vol"] = final_vol.data
+            h5f["volume1"] = volume_1.data
+            h5f["volume2"] = volume_2.data
+        numpy.testing.assert_almost_equal(
+            raw_volume,
+            final_vol.data,
+        )
+
+
+def test_get_overlap_areas():
+    """test get_overlap_areas function"""
+    f_upper = numpy.linspace(7, 15, num=9, endpoint=True)
+    f_lower = numpy.linspace(0, 12, num=13, endpoint=True)
+
+    o_1, o_2 = ZStitcher.get_overlap_areas(
+        upper_frame=f_upper,
+        lower_frame=f_lower,
+        upper_frame_key_line=3,
+        lower_frame_key_line=10,
+        overlap_size=4,
+        stitching_axis=0,
+    )
+
+    numpy.testing.assert_array_equal(o_1, o_2)
+    numpy.testing.assert_array_equal(o_1, numpy.linspace(8, 11, num=4, endpoint=True))
+
+
+def test_frame_flip(tmp_path):
+    """check it with some NXtomo fliped"""
+    pytest.skip(reason="Broken test")
+    ref_frame_width = 280
+    n_proj = 10
+    raw_frame_width = 100
+    ref_frame = PhantomGenerator.get2DPhantomSheppLogan(n=ref_frame_width).astype(numpy.float32) * 256.0
+    # create raw data
+    frame_0_shift = (0, 0)
+    frame_1_shift = (-90, 0)
+    frame_2_shift = (-180, 0)
+
+    frame_0 = scipy_shift(ref_frame, shift=frame_0_shift)[:raw_frame_width]
+    frame_1 = scipy_shift(ref_frame, shift=frame_1_shift)[:raw_frame_width]
+    frame_2 = scipy_shift(ref_frame, shift=frame_2_shift)[:raw_frame_width]
+    frames = frame_0, frame_1, frame_2
+
+    x_flips = [False, True, True]
+    y_flips = [False, False, True]
+
+    def apply_flip(args):
+        frame, flip_x, flip_y = args
+        if flip_x:
+            frame = numpy.fliplr(frame)
+        if flip_y:
+            frame = numpy.flipud(frame)
+        return frame
+
+    frames = map(apply_flip, zip(frames, x_flips, y_flips))
+
+    # create a Nxtomo for each of those raw data
+    raw_data_dir = tmp_path / "raw_data"
+    raw_data_dir.mkdir()
+    output_dir = tmp_path / "output_dir"
+    output_dir.mkdir()
+    z_position = (90, 0, -90)
+
+    scans = []
+    for (i_frame, frame), z_pos, x_flip, y_flip in zip(enumerate(frames), z_position, x_flips, y_flips):
+        nx_tomo = NXtomo()
+        nx_tomo.sample.z_translation = [z_pos] * n_proj
+        nx_tomo.sample.rotation_angle = numpy.linspace(0, 180, num=n_proj, endpoint=False)
+        nx_tomo.instrument.detector.image_key_control = [ImageKey.PROJECTION] * n_proj
+        nx_tomo.instrument.detector.x_pixel_size = 1.0
+        nx_tomo.instrument.detector.y_pixel_size = 1.0
+        nx_tomo.instrument.detector.distance = 2.3
+        if x_flip:
+            nx_tomo.instrument.detector.transformations.add_transformation(LRDetTransformation())
+        if y_flip:
+            nx_tomo.instrument.detector.transformations.add_transformation(UDDetTransformation())
+        nx_tomo.energy = 19.2
+        nx_tomo.instrument.detector.data = numpy.asarray([frame] * n_proj)
+
+        file_path = os.path.join(raw_data_dir, f"nxtomo_{i_frame}.nx")
+        entry = f"entry000{i_frame}"
+        nx_tomo.save(file_path=file_path, data_path=entry)
+        scans.append(NXtomoScan(scan=file_path, entry=entry))
+
+    output_file_path = os.path.join(output_dir, "stitched.nx")
+    output_data_path = "stitched"
+    assert len(scans) == 3
+    z_stich_config = PreProcessedZStitchingConfiguration(
+        axis_0_pos_px=(0, -90, -180),
+        axis_1_pos_px=None,
+        axis_2_pos_px=(0, 0, 0),
+        axis_0_pos_mm=None,
+        axis_1_pos_mm=None,
+        axis_2_pos_mm=None,
+        axis_0_params={},
+        axis_1_params={},
+        axis_2_params={},
+        stitching_strategy=OverlapStitchingStrategy.LINEAR_WEIGHTS,
+        overwrite_results=True,
+        input_scans=scans,
+        output_file_path=output_file_path,
+        output_data_path=output_data_path,
+        output_nexus_version=None,
+        slices=None,
+        slurm_config=None,
+        slice_for_cross_correlation="middle",
+        pixel_size=None,
+    )
+    stitcher = PreProcessZStitcher(z_stich_config)
+    output_identifier = stitcher.stitch()
+    assert output_identifier.file_path == output_file_path
+    assert output_identifier.data_path == output_data_path
+
+    created_nx_tomo = NXtomo().load(
+        file_path=output_identifier.file_path,
+        data_path=output_identifier.data_path,
+        detector_data_as="as_numpy_array",
+    )
+
+    assert created_nx_tomo.instrument.detector.data.ndim == 3
+    # insure flipping has been taking into account
+    numpy.testing.assert_array_almost_equal(ref_frame, created_nx_tomo.instrument.detector.data[0, :ref_frame_width, :])
+
+    assert len(created_nx_tomo.instrument.detector.transformations) == 0
+
+
+@pytest.mark.parametrize("alignment_axis_2", ("left", "right", "center"))
+def test_vol_z_stitching_with_alignment_axis_2(tmp_path, alignment_axis_2):
+    """
+    test z volume stitching with different width (and so that requires image alignment over axis 2)
+    """
+    # create some random data.
+    raw_volume = build_raw_volume()
+    # create folder to save data (and debug)
+    raw_data_dir = tmp_path / "raw_data"
+    raw_data_dir.mkdir()
+    output_dir = tmp_path / "output_dir"
+    output_dir.mkdir()
+
+    # create a simple case where the volume have 10 voxel of overlap and a height (z) of 30 Voxels, 40 and 30 Voxels
+    vol_1_constructor_params = {
+        "data": raw_volume[0:30, :, 4:-4],
+        "metadata": {
+            "processing_options": {
+                "reconstruction": {
+                    "position": (-15.0, 0.0, 0.0),
+                    "voxel_size_cm": (100.0, 100.0, 100.0),
+                }
+            },
+        },
+    }
+
+    vol_2_constructor_params = {
+        "data": raw_volume[20:80, :, :],
+        "metadata": {
+            "processing_options": {
+                "reconstruction": {
+                    "position": (-50.0, 0.0, 0.0),
+                    "voxel_size_cm": (100.0, 100.0, 100.0),
+                }
+            },
+        },
+    }
+
+    vol_3_constructor_params = {
+        "data": raw_volume[60:, :, 10:-10],
+        "metadata": {
+            "processing_options": {
+                "reconstruction": {
+                    "position": (-90.0, 0.0, 0.0),
+                    "voxel_size_cm": (100.0, 100.0, 100.0),
+                }
+            },
+        },
+    }
+
+    raw_volumes = []
+    axis_0_positions = []
+    for i_vol, vol_params in enumerate([vol_1_constructor_params, vol_2_constructor_params, vol_3_constructor_params]):
+        vol_params.update(
+            {
+                "file_path": os.path.join(raw_data_dir, f"raw_volume_{i_vol}.hdf5"),
+                "data_path": "volume",
+            }
+        )
+        axis_0_positions.append(vol_params["metadata"]["processing_options"]["reconstruction"]["position"][0])
+        volume = HDF5Volume(**vol_params)
+        volume.save()
+        raw_volumes.append(volume)
+
+    volume_1, volume_2, volume_3 = raw_volumes
+
+    output_volume = HDF5Volume(
+        file_path=os.path.join(output_dir, "stitched_volume.hdf5"),
+        data_path="stitched_volume",
+    )
+
+    z_stich_config = PostProcessedZStitchingConfiguration(
+        stitching_strategy=OverlapStitchingStrategy.LINEAR_WEIGHTS,
+        overwrite_results=True,
+        input_volumes=(volume_1, volume_2, volume_3),
+        output_volume=output_volume,
+        slices=None,
+        slurm_config=None,
+        axis_0_pos_px=axis_0_positions,
+        axis_0_pos_mm=None,
+        axis_0_params={"img_reg_method": ShiftAlgorithm.NONE},
+        axis_1_pos_px=None,
+        axis_1_pos_mm=None,
+        axis_1_params={"img_reg_method": ShiftAlgorithm.NONE},
+        axis_2_pos_px=None,
+        axis_2_pos_mm=None,
+        axis_2_params={"img_reg_method": ShiftAlgorithm.NONE},
+        slice_for_cross_correlation="middle",
+        voxel_size=None,
+        alignment_axis_2=AlignmentAxis2.from_value(alignment_axis_2),
+    )
+
+    stitcher = PostProcessZStitcher(z_stich_config, progress=None)
+    output_identifier = stitcher.stitch()
+    assert output_identifier.file_path == output_volume.file_path
+    assert output_identifier.data_path == output_volume.data_path
+
+    output_volume.load_data(store=True)
+    output_volume.load_metadata(store=True)
+
+    assert output_volume.data.shape == (120, 4, 120)
+
+    import h5py
+
+    with h5py.File("input.h5", mode="w") as h5f:
+        h5f["data"] = raw_volume
+
+    with h5py.File("output.h5", mode="w") as h5f:
+        h5f["data"] = output_volume.data
+
+    if alignment_axis_2 == "center":
+        numpy.testing.assert_array_almost_equal(raw_volume[:, :, 10:-10], output_volume.data[:, :, 10:-10])
+    elif alignment_axis_2 == "left":
+        numpy.testing.assert_array_almost_equal(raw_volume[:, :, :-20], output_volume.data[:, :, :-20])
+    elif alignment_axis_2 == "right":
+        numpy.testing.assert_array_almost_equal(raw_volume[:, :, 20:], output_volume.data[:, :, 20:])
+
+
+@pytest.mark.parametrize("alignment_axis_1", ("front", "center", "back"))
+def test_vol_z_stitching_with_alignment_axis_1(tmp_path, alignment_axis_1):
+    """
+    test z volume stitching with different number of frames (and so that requires image alignment over axis 0)
+    """
+    # create some random data.
+    raw_volume = build_raw_volume()
+
+    # create folder to save data (and debug)
+    raw_data_dir = tmp_path / "raw_data"
+    raw_data_dir.mkdir()
+    output_dir = tmp_path / "output_dir"
+    output_dir.mkdir()
+
+    # create a simple case where the volume have 10 voxel of overlap and a height (z) of 30 Voxels, 40 and 30 Voxels
+    vol_1_constructor_params = {
+        "data": raw_volume[
+            0:30,
+            1:3,
+        ],
+        "metadata": {
+            "processing_options": {
+                "reconstruction": {
+                    "position": (-15.0, 0.0, 0.0),
+                    "voxel_size_cm": (100.0, 100.0, 100.0),
+                }
+            },
+        },
+    }
+
+    vol_2_constructor_params = {
+        "data": raw_volume[20:80, :, :],
+        "metadata": {
+            "processing_options": {
+                "reconstruction": {
+                    "position": (-50.0, 0.0, 0.0),
+                    "voxel_size_cm": (100.0, 100.0, 100.0),
+                }
+            },
+        },
+    }
+
+    vol_3_constructor_params = {
+        "data": raw_volume[
+            60:,
+            1:3,
+        ],
+        "metadata": {
+            "processing_options": {
+                "reconstruction": {
+                    "position": (-90.0, 0.0, 0.0),
+                    "voxel_size_cm": (100.0, 100.0, 100.0),
+                }
+            },
+        },
+    }
+
+    raw_volumes = []
+    axis_0_positions = []
+    for i_vol, vol_params in enumerate([vol_1_constructor_params, vol_2_constructor_params, vol_3_constructor_params]):
+        vol_params.update(
+            {
+                "file_path": os.path.join(raw_data_dir, f"raw_volume_{i_vol}.hdf5"),
+                "data_path": "volume",
+            }
+        )
+        axis_0_positions.append(vol_params["metadata"]["processing_options"]["reconstruction"]["position"][0])
+        volume = HDF5Volume(**vol_params)
+        volume.save()
+        raw_volumes.append(volume)
+
+    volume_1, volume_2, volume_3 = raw_volumes
+
+    output_volume = HDF5Volume(
+        file_path=os.path.join(output_dir, "stitched_volume.hdf5"),
+        data_path="stitched_volume",
+    )
+
+    z_stich_config = PostProcessedZStitchingConfiguration(
+        stitching_strategy=OverlapStitchingStrategy.LINEAR_WEIGHTS,
+        overwrite_results=True,
+        input_volumes=(volume_1, volume_2, volume_3),
+        output_volume=output_volume,
+        slices=None,
+        slurm_config=None,
+        axis_0_pos_px=axis_0_positions,
+        axis_0_pos_mm=None,
+        axis_0_params={"img_reg_method": ShiftAlgorithm.NONE},
+        axis_1_pos_px=None,
+        axis_1_pos_mm=None,
+        axis_1_params={"img_reg_method": ShiftAlgorithm.NONE},
+        axis_2_pos_px=None,
+        axis_2_pos_mm=None,
+        axis_2_params={"img_reg_method": ShiftAlgorithm.NONE},
+        slice_for_cross_correlation="middle",
+        voxel_size=None,
+        alignment_axis_1=AlignmentAxis1.from_value(alignment_axis_1),
+    )
+
+    stitcher = PostProcessZStitcher(z_stich_config, progress=None)
+    output_identifier = stitcher.stitch()
+    assert output_identifier.file_path == output_volume.file_path
+    assert output_identifier.data_path == output_volume.data_path
+
+    output_volume.load_data(store=True)
+    output_volume.load_metadata(store=True)
+
+    assert output_volume.data.shape == (120, 4, 120)
+
+    if alignment_axis_1 == "middle":
+        numpy.testing.assert_array_almost_equal(raw_volume[:, 10:-10, :], output_volume.data[:, 10:-10, :])
+    elif alignment_axis_1 == "front":
+        numpy.testing.assert_array_almost_equal(raw_volume[:, :-20, :], output_volume.data[:, :-20, :])
+    elif alignment_axis_1 == "middle":
+        numpy.testing.assert_array_almost_equal(raw_volume[:, 20:, :], output_volume.data[:, 20:, :])
+
+
+def test_normalization_by_sample(tmp_path):
+    """
+    simple test of a volume stitching.
+    Raw volumes have 'extra' values (+2, +5, +9) that must be removed at the end thanks to the normalization
+    """
+    from copy import deepcopy
+
+    raw_volume = build_raw_volume()
+    # create folder to save data (and debug)
+    raw_data_dir = tmp_path / "raw_data"
+    raw_data_dir.mkdir()
+    output_dir = tmp_path / "output_dir"
+    output_dir.mkdir()
+
+    # create a simple case where the volume have 10 voxel of overlap and a height (z) of 30 Voxels, 40 and 30 Voxels
+    vol_1_constructor_params = {
+        "data": raw_volume[0:30, :, :] + 3,
+        "metadata": {
+            "processing_options": {
+                "reconstruction": {
+                    "position": (-15.0, 0.0, 0.0),
+                    "voxel_size_cm": (100.0, 100.0, 100.0),
+                }
+            },
+        },
+    }
+
+    vol_2_constructor_params = {
+        "data": raw_volume[20:80, :, :] + 5,
+        "metadata": {
+            "processing_options": {
+                "reconstruction": {
+                    "position": (-50.0, 0.0, 0.0),
+                    "voxel_size_cm": (100.0, 100.0, 100.0),
+                }
+            },
+        },
+    }
+
+    vol_3_constructor_params = {
+        "data": raw_volume[60:, :, :] + 12,
+        "metadata": {
+            "processing_options": {
+                "reconstruction": {
+                    "position": (-90.0, 0.0, 0.0),
+                    "voxel_size_cm": (100.0, 100.0, 100.0),
+                }
+            },
+        },
+    }
+
+    raw_volumes = []
+    axis_0_positions = []
+    for i_vol, vol_params in enumerate([vol_1_constructor_params, vol_2_constructor_params, vol_3_constructor_params]):
+        vol_params.update(
+            {
+                "file_path": os.path.join(raw_data_dir, f"raw_volume_{i_vol}.hdf5"),
+                "data_path": "volume",
+            }
+        )
+
+        axis_0_positions.append(vol_params["metadata"]["processing_options"]["reconstruction"]["position"][0])
+
+        volume = HDF5Volume(**vol_params)
+        volume.save()
+        raw_volumes.append(volume)
+
+    volume_1, volume_2, volume_3 = raw_volumes
+
+    output_volume = HDF5Volume(
+        file_path=os.path.join(output_dir, "stitched_volume.hdf5"),
+        data_path="stitched_volume",
+    )
+
+    normalization_by_sample = NormalizationBySample()
+    normalization_by_sample.set_is_active(True)
+    normalization_by_sample.width = 1
+    normalization_by_sample.margin = 0
+    normalization_by_sample.side = "left"
+    normalization_by_sample.method = "median"
+
+    z_stich_config = PostProcessedZStitchingConfiguration(
+        stitching_strategy=OverlapStitchingStrategy.CLOSEST,
+        overwrite_results=True,
+        input_volumes=(volume_1, volume_2, volume_3),
+        output_volume=output_volume,
+        slices=None,
+        slurm_config=None,
+        axis_0_pos_px=axis_0_positions,
+        axis_0_pos_mm=None,
+        axis_0_params={"img_reg_method": ShiftAlgorithm.NONE},
+        axis_1_pos_px=None,
+        axis_1_pos_mm=None,
+        axis_1_params={"img_reg_method": ShiftAlgorithm.NONE},
+        axis_2_pos_px=None,
+        axis_2_pos_mm=None,
+        axis_2_params={"img_reg_method": ShiftAlgorithm.NONE},
+        slice_for_cross_correlation="middle",
+        voxel_size=None,
+        normalization_by_sample=normalization_by_sample,
+    )
+
+    stitcher = PostProcessZStitcher(z_stich_config, progress=None)
+    output_identifier = stitcher.stitch()
+
+    assert output_identifier.file_path == output_volume.file_path
+    assert output_identifier.data_path == output_volume.data_path
+
+    output_volume.data = None
+    output_volume.metadata = None
+    output_volume.load_data(store=True)
+    output_volume.load_metadata(store=True)
+
+    assert raw_volume.shape == output_volume.data.shape
+
+    numpy.testing.assert_array_almost_equal(raw_volume, output_volume.data)
+
+    metadata = output_volume.metadata
+    assert metadata["program"] == "nabu-stitching"
+    assert "configuration" in metadata
+    assert output_volume.position[0] == -60.0
+    assert output_volume.pixel_size == (1.0, 1.0, 1.0)